| HPO | Cluster | Description |
|---|---|---|
| HP:0003540 | 1 | Impaired platelet aggregation |
| HP:0003655 | 1 | Reduced level of N-acetylglucosaminyltransferase II |
| HP:0500173 | 1 | Reflex asystolic syncope |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 1 | hsa00513 | Various types of N-glycan biosynthesis | 100 | MGAT2 |
| 1 | hsa00510 | N-Glycan biosynthesis | 100 | MGAT2 |
| 1 | R-HSA-9694635 | Translation of Structural Proteins | 100 | MGAT2 |
| 1 | R-HSA-9694548 | Maturation of spike protein | 100 | MGAT2 |
| 1 | R-HSA-3781865 | Diseases of glycosylation | 100 | MGAT2 |
| 1 | R-HSA-5668914 | Diseases of metabolism | 100 | MGAT2 |
| 1 | R-HSA-446203 | Asparagine N-linked glycosylation | 100 | MGAT2 |
| 1 | R-HSA-3781860 | Diseases associated with N-glycosylation of proteins | 100 | MGAT2 |
| 1 | R-HSA-975578 | Reactions specific to the complex N-glycan synthesis pathway | 100 | MGAT2 |
| 1 | R-HSA-9772573 | Late SARS-CoV-2 Infection Events | 100 | MGAT2 |
| 1 | R-HSA-975576 | N-glycan antennae elongation in the medial/trans-Golgi | 100 | MGAT2 |
| 1 | R-HSA-9679506 | SARS-CoV Infections | 100 | MGAT2 |
| 1 | R-HSA-9694516 | SARS-CoV-2 Infection | 100 | MGAT2 |
| 1 | R-HSA-948021 | Transport to the Golgi and subsequent modification | 100 | MGAT2 |
| 1 | GO:0018279 | protein N-linked glycosylation via asparagine | 100 | MGAT2 |
| 1 | GO:0019082 | viral protein processing | 100 | MGAT2 |
| 1 | GO:0009312 | oligosaccharide biosynthetic process | 100 | MGAT2 |
| 1 | GO:0008375 | acetylglucosaminyltransferase activity | 100 | MGAT2 |
| 1 | GO:0030145 | manganese ion binding | 100 | MGAT2 |
| 1 | GO:0140103 | catalytic activity, acting on a glycoprotein | 100 | MGAT2 |
| 1 | GO:0005795 | Golgi stack | 100 | MGAT2 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0007456 | 4 | Progressive reticulate hyperpigmentation |
| HP:0012855 | 4 | Scrotal hyperpigmentation |
| HP:0030442 | 4 | Anal margin squamous cell carcinoma |
| HP:0031293 | 4 | Digital pitting scar |
| HP:0031525 | 4 | Keratoacanthoma |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 4 | hsa00514 | Other types of O-glycan biosynthesis | 100 | POGLUT1, POFUT1 |
| 4 | hsa04330 | Notch signaling pathway | 100 | PSENEN |
| 4 | R-HSA-2122948 | Activated NOTCH1 Transmits Signal to the Nucleus | 100 | PSENEN |
| 4 | R-HSA-2644603 | Signaling by NOTCH1 in Cancer | 100 | PSENEN |
| 4 | R-HSA-2979096 | NOTCH2 Activation and Transmission of Signal to the Nucleus | 100 | PSENEN |
| 4 | R-HSA-2682334 | EPH-Ephrin signaling | 100 | PSENEN |
| 4 | R-HSA-3928665 | EPH-ephrin mediated repulsion of cells | 100 | PSENEN |
| 4 | R-HSA-204998 | Cell death signalling via NRAGE, NRIF and NADE | 100 | PSENEN |
| 4 | R-HSA-193704 | p75 NTR receptor-mediated signalling | 100 | PSENEN |
| 4 | R-HSA-9013700 | NOTCH4 Activation and Transmission of Signal to the Nucleus | 100 | PSENEN |
| 4 | R-HSA-1251985 | Nuclear signaling by ERBB4 | 100 | PSENEN |
| 4 | R-HSA-2644602 | Signaling by NOTCH1 PEST Domain Mutants in Cancer | 100 | PSENEN |
| 4 | R-HSA-2894858 | Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer | 100 | PSENEN |
| 4 | R-HSA-446728 | Cell junction organization | 100 | KRT5 |
| 4 | R-HSA-205043 | NRIF signals cell death from the nucleus | 100 | PSENEN |
| 4 | R-HSA-9013694 | Signaling by NOTCH4 | 100 | PSENEN |
| 4 | R-HSA-193692 | Regulated proteolysis of p75NTR | 100 | PSENEN |
| 4 | R-HSA-446107 | Type I hemidesmosome assembly | 100 | KRT5 |
| 4 | R-HSA-1980145 | Signaling by NOTCH2 | 100 | PSENEN |
| 4 | R-HSA-1912422 | Pre-NOTCH Expression and Processing | 100 | POGLUT1, POFUT1 |
| 4 | R-HSA-157118 | Signaling by NOTCH | 100 | POGLUT1, PSENEN, POFUT1 |
| 4 | R-HSA-1980143 | Signaling by NOTCH1 | 100 | PSENEN |
| 4 | R-HSA-9012852 | Signaling by NOTCH3 | 100 | PSENEN |
| 4 | R-HSA-977225 | Amyloid fiber formation | 100 | PSENEN |
| 4 | R-HSA-2894862 | Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants | 100 | PSENEN |
| 4 | R-HSA-1236394 | Signaling by ERBB4 | 100 | PSENEN |
| 4 | R-HSA-9013507 | NOTCH3 Activation and Transmission of Signal to the Nucleus | 100 | PSENEN |
| 4 | R-HSA-2644606 | Constitutive Signaling by NOTCH1 PEST Domain Mutants | 100 | PSENEN |
| 4 | GO:0010470 | regulation of gastrulation | 100 | POGLUT1 |
| 4 | GO:0031293 | membrane protein intracellular domain proteolysis | 100 | PSENEN |
| 4 | GO:0034205 | amyloid-beta formation | 100 | PSENEN |
| 4 | GO:0006509 | membrane protein ectodomain proteolysis | 100 | PSENEN |
| 4 | GO:0048339 | paraxial mesoderm development | 100 | POGLUT1 |
| 4 | GO:0010950 | positive regulation of endopeptidase activity | 100 | PSENEN |
| 4 | GO:0031424 | keratinization | 100 | KRT5 |
| 4 | GO:0036065 | fucosylation | 100 | POFUT1 |
| 4 | GO:0016266 | O-glycan processing | 100 | POFUT1 |
| 4 | GO:0045747 | positive regulation of Notch signaling pathway | 100 | POGLUT1 |
| 4 | GO:0001756 | somitogenesis | 100 | POGLUT1, POFUT1 |
| 4 | GO:0018242 | protein O-linked glycosylation via serine | 100 | POGLUT1 |
| 4 | GO:0045109 | intermediate filament organization | 100 | KRT5 |
| 4 | GO:0006004 | fucose metabolic process | 100 | POFUT1 |
| 4 | GO:0030280 | structural constituent of skin epidermis | 100 | KRT5 |
| 4 | GO:0061133 | endopeptidase activator activity | 100 | PSENEN |
| 4 | GO:0005200 | structural constituent of cytoskeleton | 100 | KRT5 |
| 4 | GO:0035252 | UDP-xylosyltransferase activity | 100 | POGLUT1 |
| 4 | GO:0008417 | fucosyltransferase activity | 100 | POFUT1 |
| 4 | GO:0097110 | scaffold protein binding | 100 | KRT5 |
| 4 | GO:0035251 | UDP-glucosyltransferase activity | 100 | POGLUT1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000517 | 7 | Abnormal lens morphology |
| HP:0006152 | 7 | Proximal symphalangism of hands |
| HP:0009608 | 7 | Complete duplication of proximal phalanx of the thumb |
| HP:0009966 | 7 | Complete duplication of the middle phalanx of the 3rd finger |
| HP:0009970 | 7 | Partial duplication of the proximal phalanx of the 3rd finger |
| HP:0100266 | 7 | Synostosis of carpals/tarsals |
| HP:0100345 | 7 | Tibial deviation of the 2nd toe |
| HP:0100347 | 7 | Tibial deviation of the 5th toe |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 7 | hsa00532 | Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | 100 | CHSY1 |
| 7 | R-HSA-3781865 | Diseases of glycosylation | 100 | CHSY1 |
| 7 | R-HSA-2022870 | Chondroitin sulfate biosynthesis | 100 | CHSY1 |
| 7 | R-HSA-5668914 | Diseases of metabolism | 100 | CHSY1 |
| 7 | R-HSA-1793185 | Chondroitin sulfate/dermatan sulfate metabolism | 100 | CHSY1 |
| 7 | R-HSA-71387 | Metabolism of carbohydrates | 100 | CHSY1 |
| 7 | R-HSA-3560782 | Diseases associated with glycosaminoglycan metabolism | 100 | CHSY1 |
| 7 | R-HSA-1630316 | Glycosaminoglycan metabolism | 100 | CHSY1 |
| 7 | GO:0051923 | sulfation | 100 | CHSY1 |
| 7 | GO:0045880 | positive regulation of smoothened signaling pathway | 100 | CHSY1 |
| 7 | GO:0009954 | proximal/distal pattern formation | 100 | CHSY1 |
| 7 | GO:0060349 | bone morphogenesis | 100 | CHSY1 |
| 7 | GO:0031667 | response to nutrient levels | 100 | CHSY1 |
| 7 | GO:0002063 | chondrocyte development | 100 | CHSY1 |
| 7 | GO:0030279 | negative regulation of ossification | 100 | CHSY1 |
| 7 | GO:0030206 | chondroitin sulfate biosynthetic process | 100 | CHSY1 |
| 7 | GO:0008376 | acetylgalactosaminyltransferase activity | 100 | CHSY1 |
| 7 | GO:0015020 | glucuronosyltransferase activity | 100 | CHSY1 |
| 7 | GO:0032580 | Golgi cisterna membrane | 100 | CHSY1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000793 | 16 | Membranoproliferative glomerulonephritis |
| HP:0004430 | 16 | Severe combined immunodeficiency |
| HP:0008587 | 16 | Mild neurosensory hearing impairment |
| HP:0031292 | 16 | Cutaneous abscess |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 16 | GO:0009226 | nucleotide-sugar biosynthetic process | 100 | PGM3 |
| 16 | GO:1901071 | glucosamine-containing compound metabolic process | 100 | PGM3 |
| 16 | GO:0046349 | amino sugar biosynthetic process | 100 | PGM3 |
| 16 | GO:0006047 | UDP-N-acetylglucosamine metabolic process | 100 | PGM3 |
| 16 | hsa01250 | Biosynthesis of nucleotide sugars | 75 | PGM3 |
| 16 | hsa00520 | Amino sugar and nucleotide sugar metabolism | 75 | PGM3 |
| 16 | R-HSA-446219 | Synthesis of substrates in N-glycan biosythesis | 75 | PGM3 |
| 16 | R-HSA-446203 | Asparagine N-linked glycosylation | 75 | PGM3 |
| 16 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 75 | PGM3 |
| 16 | GO:0006487 | protein N-linked glycosylation | 75 | PGM3 |
| 16 | GO:0006493 | protein O-linked glycosylation | 75 | PGM3 |
| 16 | GO:0000287 | magnesium ion binding | 75 | PGM3 |
| 16 | GO:0016868 | intramolecular transferase activity, phosphotransferases | 75 | PGM3 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001407 | 18 | Hepatic cysts |
| HP:0006557 | 18 | Polycystic liver disease |
| HP:0012592 | 18 | Albuminuria |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 18 | hsa04141 | Protein processing in endoplasmic reticulum | 100 | PRKCSH, GANAB, DNAJB11, SEC63 |
| 18 | hsa00510 | N-Glycan biosynthesis | 100 | ALG9, GANAB, ALG5 |
| 18 | R-HSA-5620916 | VxPx cargo-targeting to cilium | 100 | PKD2, PKD1 |
| 18 | R-HSA-446203 | Asparagine N-linked glycosylation | 100 | PRKCSH, ALG9, GANAB, ALG5 |
| 18 | R-HSA-5620920 | Cargo trafficking to the periciliary membrane | 100 | PKD2, PKD1 |
| 18 | R-HSA-5617833 | Cilium Assembly | 100 | IFT140, PKD2, PKD1 |
| 18 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 100 | ALG9, ALG5 |
| 18 | R-HSA-1852241 | Organelle biogenesis and maintenance | 100 | IFT140, PKD2, PKD1 |
| 18 | GO:0072176 | nephric duct development | 100 | PKD1, PKD2 |
| 18 | GO:0021510 | spinal cord development | 100 | PKD1, PKD2 |
| 18 | GO:0007204 | positive regulation of cytosolic calcium ion concentration | 100 | PKD1, PKD2 |
| 18 | GO:0060315 | negative regulation of ryanodine-sensitive calcium-release channel activity | 100 | PKD2 |
| 18 | GO:0048754 | branching morphogenesis of an epithelial tube | 100 | LRP5, PKD1, PKD2 |
| 18 | GO:0072017 | distal tubule development | 100 | PKD1, PKD2 |
| 18 | GO:0001889 | liver development | 100 | PKD1, PRKCSH, SEC63, PKD2 |
| 18 | GO:0072173 | metanephric tubule morphogenesis | 100 | PKD1 |
| 18 | GO:0072014 | proximal tubule development | 100 | PKD1 |
| 18 | GO:0035845 | photoreceptor cell outer segment organization | 100 | IFT140 |
| 18 | GO:0072078 | nephron tubule morphogenesis | 100 | PKD1, PKD2 |
| 18 | GO:0018279 | protein N-linked glycosylation via asparagine | 100 | ALG5 |
| 18 | GO:0021915 | neural tube development | 100 | TSC2, TSC1, PKD1, IFT140, PKD2 |
| 18 | GO:2000045 | regulation of G1/S transition of mitotic cell cycle | 100 | PKD1, PKD2 |
| 18 | GO:0050982 | detection of mechanical stimulus | 100 | PKD1, PKD2 |
| 18 | GO:0072164 | mesonephric tubule development | 100 | PKD1, PKD2 |
| 18 | GO:0007259 | receptor signaling pathway via JAK-STAT | 100 | PKD1, IFNG, PKD2 |
| 18 | GO:0001502 | cartilage condensation | 100 | PKD1 |
| 18 | GO:0006488 | dolichol-linked oligosaccharide biosynthetic process | 100 | ALG9 |
| 18 | GO:1990403 | embryonic brain development | 100 | IFT140 |
| 18 | GO:0009415 | response to water | 100 | PKD2 |
| 18 | GO:0001892 | embryonic placenta development | 100 | PKD1, PKD2 |
| 18 | GO:0072070 | loop of Henle development | 100 | PKD1, PKD2 |
| 18 | GO:0072273 | metanephric nephron morphogenesis | 100 | PKD1, PKD2 |
| 18 | GO:0019348 | dolichol metabolic process | 100 | ALG9 |
| 18 | GO:0060972 | left/right pattern formation | 100 | BICC1, IFT140, ALG5, PKD2 |
| 18 | GO:0045737 | positive regulation of cyclin-dependent protein serine/threonine kinase activity | 100 | PKD1, PKD2 |
| 18 | GO:0072234 | metanephric nephron tubule development | 100 | PKD1, PKD2 |
| 18 | GO:0048562 | embryonic organ morphogenesis | 100 | IFT140, PKD2 |
| 18 | GO:0071498 | cellular response to fluid shear stress | 100 | PKD2 |
| 18 | GO:0072205 | metanephric collecting duct development | 100 | PKD1 |
| 18 | GO:0035721 | intraciliary retrograde transport | 100 | IFT140 |
| 18 | GO:0072075 | metanephric mesenchyme development | 100 | PKD2 |
| 18 | GO:0006491 | N-glycan processing | 100 | GANAB, PRKCSH |
| 18 | GO:0016055 | Wnt signaling pathway | 100 | TSC2, PKD1, PKD2, LRP5, BICC1 |
| 18 | GO:0036303 | lymph vessel morphogenesis | 100 | PKD1 |
| 18 | GO:0007368 | determination of left/right symmetry | 100 | BICC1, IFT140, ALG5, PKD2 |
| 18 | GO:0051290 | protein heterotetramerization | 100 | PKD1, PKD2 |
| 18 | GO:0060674 | placenta blood vessel development | 100 | PKD1, PKD2 |
| 18 | GO:0042994 | cytoplasmic sequestering of transcription factor | 100 | PKD1, PKD2 |
| 18 | GO:0035251 | UDP-glucosyltransferase activity | 100 | ALG5 |
| 18 | GO:0015926 | glucosidase activity | 100 | GANAB |
| 18 | GO:0051787 | misfolded protein binding | 100 | DNAJB11 |
| 18 | GO:0005248 | voltage-gated sodium channel activity | 100 | PKD2 |
| 18 | GO:0030246 | carbohydrate binding | 100 | GANAB, PKD1 |
| 18 | GO:0051371 | muscle alpha-actinin binding | 100 | PKD2 |
| 18 | GO:0000030 | mannosyltransferase activity | 100 | ALG9 |
| 18 | GO:0015271 | outward rectifier potassium channel activity | 100 | PKD2 |
| 18 | GO:0044325 | transmembrane transporter binding | 100 | PRKCSH, PKD1, PKD2 |
| 18 | GO:0015278 | calcium-release channel activity | 100 | PKD2 |
| 18 | GO:0042813 | Wnt receptor activity | 100 | PKD1, LRP5 |
| 18 | GO:0032391 | photoreceptor connecting cilium | 100 | IFT140 |
| 18 | GO:0036064 | ciliary basal body | 100 | PKD2, IFT140 |
| 18 | GO:0005788 | endoplasmic reticulum lumen | 100 | GANAB, DNAJB11, PRKCSH |
| 18 | GO:0034663 | endoplasmic reticulum chaperone complex | 100 | DNAJB11 |
| 18 | GO:0101031 | protein folding chaperone complex | 100 | DNAJB11, TSC1 |
| 18 | GO:0034703 | cation channel complex | 100 | PKD2, PKD1 |
| 18 | GO:0060170 | ciliary membrane | 100 | PKD2, PKD1 |
| 18 | GO:0097542 | ciliary tip | 100 | IFT140 |
| 18 | GO:0097730 | non-motile cilium | 100 | PKD2, IFT140 |
| 18 | GO:0098553 | lumenal side of endoplasmic reticulum membrane | 100 | PKD2 |
| 18 | GO:0031514 | motile cilium | 100 | PKD2, PKD1 |
| 18 | GO:0098554 | cytoplasmic side of endoplasmic reticulum membrane | 100 | PKD2 |
| 18 | GO:0016323 | basolateral plasma membrane | 100 | PKD2, PKD1 |
| 18 | GO:0099738 | cell cortex region | 100 | PKD2 |
| 18 | GO:0030990 | intraciliary transport particle | 100 | IFT140 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0003325 | 41 | Limb-girdle muscle weakness |
| HP:0003403 | 41 | EMG: decremental response of compound muscle action potential to repetitive nerve stimulation |
| HP:0009028 | 41 | Generalized weakness of limb muscles |
| HP:0030191 | 41 | Abnormal peripheral nervous system synaptic transmission |
| HP:0030202 | 41 | Favorable response of weakness to acetylcholine esterase inhibitors |
| HP:0030205 | 41 | Increased jitter at single fiber EMG |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 41 | hsa01250 | Biosynthesis of nucleotide sugars | 100.00000 | GMPPB, GFPT1 |
| 41 | hsa00520 | Amino sugar and nucleotide sugar metabolism | 100.00000 | GMPPB, GFPT1 |
| 41 | R-HSA-3781865 | Diseases of glycosylation | 100.00000 | DPAGT1, GFPT1, AGRN, ALG2, ALG14, POMT1 |
| 41 | R-HSA-446219 | Synthesis of substrates in N-glycan biosythesis | 100.00000 | GMPPB, GFPT1 |
| 41 | R-HSA-5668914 | Diseases of metabolism | 100.00000 | DPAGT1, GFPT1, AGRN, ALG2, ALG14, POMT1 |
| 41 | R-HSA-446203 | Asparagine N-linked glycosylation | 100.00000 | DPAGT1, GMPPB, GFPT1, ALG2, ALG14 |
| 41 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 100.00000 | DPAGT1, GMPPB, GFPT1, ALG2, ALG14 |
| 41 | GO:0009226 | nucleotide-sugar biosynthetic process | 100.00000 | GFPT1, GMPPB |
| 41 | hsa00513 | Various types of N-glycan biosynthesis | 83.33333 | ALG2, ALG14 |
| 41 | hsa00510 | N-Glycan biosynthesis | 83.33333 | ALG2, DPAGT1, ALG14 |
| 41 | R-HSA-3781860 | Diseases associated with N-glycosylation of proteins | 83.33333 | DPAGT1, ALG2, ALG14 |
| 41 | GO:0006488 | dolichol-linked oligosaccharide biosynthetic process | 83.33333 | ALG2, DPAGT1, ALG14 |
| 41 | GO:0006047 | UDP-N-acetylglucosamine metabolic process | 83.33333 | GFPT1, DPAGT1 |
| 41 | GO:0019348 | dolichol metabolic process | 83.33333 | ALG2, DPAGT1, ALG14 |
| 41 | GO:0006112 | energy reserve metabolic process | 83.33333 | GFPT1, PHKB |
| 41 | GO:0016757 | glycosyltransferase activity | 83.33333 | DPAGT1, ALG14, ALG2 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000918 | 44 | Scapular exostoses |
| HP:0002318 | 44 | Cervical myelopathy |
| HP:0003406 | 44 | Peripheral nerve compression |
| HP:0003959 | 44 | Deformed forearm bones |
| HP:0003977 | 44 | Deformed radius |
| HP:0005922 | 44 | Abnormal hand morphology |
| HP:0006385 | 44 | Short lower limbs |
| HP:0008443 | 44 | Neuropathic spinal arthropathy |
| HP:0020110 | 44 | Bone fracture |
| HP:0030883 | 44 | Femoroacetabular impingement |
| HP:0031625 | 44 | Pseudoaneurysm |
| HP:0032510 | 44 | Tendon pain |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 44 | R-HSA-3656237 | Defective EXT2 causes exostoses 2 | 100.00000 | EXT2, AGRN, EXT1 |
| 44 | R-HSA-1638091 | Heparan sulfate/heparin (HS-GAG) metabolism | 100.00000 | EXT2, AGRN, EXT1 |
| 44 | R-HSA-3656253 | Defective EXT1 causes exostoses 1, TRPS2 and CHDS | 100.00000 | EXT2, AGRN, EXT1 |
| 44 | R-HSA-71387 | Metabolism of carbohydrates | 100.00000 | EXT2, EXT1, AGRN, SLC25A1, SLC26A2, GALT |
| 44 | R-HSA-3560782 | Diseases associated with glycosaminoglycan metabolism | 100.00000 | SLC26A2, EXT2, AGRN, EXT1 |
| 44 | R-HSA-1630316 | Glycosaminoglycan metabolism | 100.00000 | SLC26A2, EXT2, AGRN, EXT1 |
| 44 | R-HSA-5668914 | Diseases of metabolism | 100.00000 | EXT2, EXT1, GNE, MOGS, AGRN, GALT, SLC26A2 |
| 44 | R-HSA-3781865 | Diseases of glycosylation | 100.00000 | EXT2, EXT1, GNE, MOGS, AGRN, GALT, SLC26A2 |
| 44 | R-HSA-2022928 | HS-GAG biosynthesis | 100.00000 | EXT2, AGRN, EXT1 |
| 44 | GO:0001958 | endochondral ossification | 100.00000 | MMP13, COL13A1, MMP14, EXT1 |
| 44 | GO:0043931 | ossification involved in bone maturation | 100.00000 | EBP, EXT1 |
| 44 | hsa00534 | Glycosaminoglycan biosynthesis - heparan sulfate / heparin | 91.66667 | EXT1, EXT2 |
| 44 | GO:0072498 | embryonic skeletal joint development | 91.66667 | EXT1 |
| 44 | GO:0002063 | chondrocyte development | 91.66667 | EXT1 |
| 44 | GO:0042044 | fluid transport | 91.66667 | EXT2, EXT1 |
| 44 | GO:0000271 | polysaccharide biosynthetic process | 91.66667 | EXT2, EXT1 |
| 44 | GO:0007498 | mesoderm development | 91.66667 | EXT2, EXT1 |
| 44 | GO:0050891 | multicellular organismal-level water homeostasis | 91.66667 | EXT2, EXT1 |
| 44 | GO:0061484 | hematopoietic stem cell homeostasis | 91.66667 | EXT1 |
| 44 | GO:0032836 | glomerular basement membrane development | 91.66667 | EXT1 |
| 44 | GO:0071711 | basement membrane organization | 91.66667 | EXT1 |
| 44 | GO:0035988 | chondrocyte proliferation | 91.66667 | SLC26A2, MMP14, EXT1 |
| 44 | GO:0055078 | sodium ion homeostasis | 91.66667 | EXT2, EXT1 |
| 44 | GO:0015012 | heparan sulfate proteoglycan biosynthetic process | 91.66667 | EXT2, EXT1 |
| 44 | GO:0061744 | motor behavior | 91.66667 | EXT1 |
| 44 | GO:0050901 | leukocyte tethering or rolling | 91.66667 | EXT1 |
| 44 | GO:0003416 | endochondral bone growth | 91.66667 | MMP13, EXT1 |
| 44 | GO:0048733 | sebaceous gland development | 91.66667 | EXT1 |
| 44 | GO:0002524 | hypersensitivity | 91.66667 | EXT1 |
| 44 | GO:0031069 | hair follicle morphogenesis | 91.66667 | EXT1 |
| 44 | GO:0008217 | regulation of blood pressure | 91.66667 | GNA11, EXT2, EXT1 |
| 44 | GO:0060218 | hematopoietic stem cell differentiation | 91.66667 | EXT1 |
| 44 | GO:0021554 | optic nerve development | 91.66667 | EXT1 |
| 44 | GO:0017145 | stem cell division | 91.66667 | EXT1 |
| 44 | GO:0070593 | dendrite self-avoidance | 91.66667 | EXT1 |
| 44 | GO:0051923 | sulfation | 91.66667 | EXT2, EXT1 |
| 44 | GO:0060441 | epithelial tube branching involved in lung morphogenesis | 91.66667 | EXT1 |
| 44 | GO:0021772 | olfactory bulb development | 91.66667 | EXT1 |
| 44 | GO:0009642 | response to light intensity | 91.66667 | EXT1 |
| 44 | GO:0072112 | podocyte differentiation | 91.66667 | EXT1 |
| 44 | GO:0036336 | dendritic cell migration | 91.66667 | EXT1 |
| 44 | GO:0140962 | multicellular organismal-level chemical homeostasis | 91.66667 | EXT2, EXT1 |
| 44 | GO:0003128 | heart field specification | 91.66667 | EXT1 |
| 44 | GO:0071625 | vocalization behavior | 91.66667 | EXT1 |
| 44 | GO:0030210 | heparin biosynthetic process | 91.66667 | EXT2, EXT1 |
| 44 | GO:0060047 | heart contraction | 91.66667 | EXT2, EXT1 |
| 44 | GO:0030204 | chondroitin sulfate metabolic process | 91.66667 | EXT1 |
| 44 | GO:0060351 | cartilage development involved in endochondral bone morphogenesis | 91.66667 | MMP13, EXT1 |
| 44 | GO:0042311 | vasodilation | 91.66667 | EXT2, EXT1 |
| 44 | GO:0046982 | protein heterodimerization activity | 91.66667 | EXT2, IKBKG, EXT1 |
| 44 | GO:0008375 | acetylglucosaminyltransferase activity | 91.66667 | EXT2, EXT1 |
| 44 | GO:0015020 | glucuronosyltransferase activity | 91.66667 | EXT2, EXT1 |
| 44 | GO:0007492 | endoderm development | 83.33333 | MMP2, MMP14, EXT1, FN1 |
| 44 | GO:0035176 | social behavior | 83.33333 | EXT1 |
| 44 | GO:0007409 | axonogenesis | 83.33333 | SPART, EXT1, FN1 |
| 44 | GO:0060560 | developmental growth involved in morphogenesis | 83.33333 | SPART, EXT1, FN1 |
| 44 | GO:0001974 | blood vessel remodeling | 83.33333 | EXT1 |
| 44 | GO:1904888 | cranial skeletal system development | 83.33333 | GNA11, MMP14, EXT1 |
| 44 | GO:0042596 | fear response | 83.33333 | EXT1 |
| 44 | GO:0048588 | developmental cell growth | 83.33333 | SPART, EXT1, FN1 |
| 44 | GO:0030509 | BMP signaling pathway | 75.00000 | SPART, EXT1 |
| 44 | GO:0045453 | bone resorption | 75.00000 | EXT1 |
| 44 | GO:0001707 | mesoderm formation | 75.00000 | EXT2 |
| 44 | GO:0014033 | neural crest cell differentiation | 75.00000 | EXT1, FN1 |
| 44 | GO:0009615 | response to virus | 75.00000 | EXT1, IKBKG |
| 44 | GO:0008543 | fibroblast growth factor receptor signaling pathway | 75.00000 | FGF23, EXT1 |
| 44 | GO:0042060 | wound healing | 75.00000 | EXT1, FN1 |
| 44 | GO:0002067 | glandular epithelial cell differentiation | 75.00000 | EXT1 |
| 44 | GO:0030199 | collagen fibril organization | 75.00000 | EXT1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000973 | 49 | Cutis laxa |
| HP:0004523 | 49 | Long eyebrows |
| HP:0010814 | 49 | Abnormal position of hair whorl |
| HP:0012301 | 49 | Type II transferrin isoform profile |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 49 | hsa00510 | N-Glycan biosynthesis | 100 | ALG8, B4GALT1, MAN1B1 |
| 49 | R-HSA-3781865 | Diseases of glycosylation | 100 | B4GALT1, ALG8, MAN1B1, B4GALT7 |
| 49 | R-HSA-5668914 | Diseases of metabolism | 100 | B4GALT1, ALG8, MAN1B1, B4GALT7 |
| 49 | R-HSA-3781860 | Diseases associated with N-glycosylation of proteins | 100 | B4GALT1, ALG8, MAN1B1 |
| 49 | R-HSA-901032 | ER Quality Control Compartment (ERQC) | 100 | MAN1B1 |
| 49 | GO:0015924 | mannosyl-oligosaccharide mannosidase activity | 100 | MAN1B1 |
| 49 | GO:0044322 | endoplasmic reticulum quality control compartment | 100 | MAN1B1 |
| 49 | hsa00513 | Various types of N-glycan biosynthesis | 75 | B4GALT1, MAN1B1 |
| 49 | R-HSA-9694635 | Translation of Structural Proteins | 75 | MAN1B1 |
| 49 | R-HSA-901042 | Calnexin/calreticulin cycle | 75 | MAN1B1 |
| 49 | R-HSA-532668 | N-glycan trimming in the ER and Calnexin/Calreticulin cycle | 75 | MAN1B1 |
| 49 | R-HSA-446203 | Asparagine N-linked glycosylation | 75 | COG1, COG4, B4GALT1, MAN1B1, COG7 |
| 49 | R-HSA-9694548 | Maturation of spike protein | 75 | MAN1B1 |
| 49 | GO:0019082 | viral protein processing | 75 | MAN1B1 |
| 49 | GO:0009311 | oligosaccharide metabolic process | 75 | MAN1B1, B4GALT1 |
| 49 | GO:0006517 | protein deglycosylation | 75 | MAN1B1 |
| 49 | GO:0006516 | glycoprotein catabolic process | 75 | MAN1B1 |
| 49 | GO:1904587 | response to glycoprotein | 75 | MAN1B1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0002283 | 59 | Global brain atrophy |
| HP:0002401 | 59 | Stroke-like episode |
| HP:0010845 | 59 | EEG with generalized slow activity |
| HP:0012050 | 59 | Anasarca |
| HP:0012512 | 59 | Diffuse optic disc pallor |
| HP:0025534 | 59 | Ocular melanocytosis |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 59 | R-HSA-5668914 | Diseases of metabolism | 100.00000 | DPAGT1, RFT1, ALG13, DPM3, DOLK, CYP27A1, PMM2 |
| 59 | R-HSA-3781860 | Diseases associated with N-glycosylation of proteins | 100.00000 | DPAGT1, RFT1, ALG13 |
| 59 | hsa00510 | N-Glycan biosynthesis | 83.33333 | DPAGT1, DOLK, DPM3 |
| 59 | R-HSA-3781865 | Diseases of glycosylation | 83.33333 | DPAGT1, RFT1, DPM3, DOLK, PMM2 |
| 59 | R-HSA-446203 | Asparagine N-linked glycosylation | 83.33333 | DPAGT1, RFT1, DPM3, DOLK, PMM2 |
| 59 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 83.33333 | DPAGT1, RFT1, DPM3, DOLK, PMM2 |
| 59 | GO:0006488 | dolichol-linked oligosaccharide biosynthetic process | 83.33333 | RFT1, DPAGT1, DOLK |
| 59 | GO:0019348 | dolichol metabolic process | 83.33333 | DPM3, RFT1, DPAGT1, DOLK |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000308 | 96 | Microretrognathia |
| HP:0002761 | 96 | Generalized joint hypermobility |
| HP:0002947 | 96 | Cervical kyphosis |
| HP:0003199 | 96 | Decreased muscle mass |
| HP:0003414 | 96 | Atlantoaxial dislocation |
| HP:0005272 | 96 | Prominent nasolabial fold |
| HP:0031869 | 96 | Recurrent joint dislocation |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 96 | hsa00532 | Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | 100.00000 | CHST14, B3GALT6, DSE |
| 96 | R-HSA-1793185 | Chondroitin sulfate/dermatan sulfate metabolism | 100.00000 | CHST14, DSE, B3GALT6 |
| 96 | R-HSA-2022923 | Dermatan sulfate biosynthesis | 100.00000 | CHST14, DSE |
| 96 | GO:0050655 | dermatan sulfate proteoglycan metabolic process | 100.00000 | CHST14, DSE |
| 96 | R-HSA-71387 | Metabolism of carbohydrates | 85.71429 | GYG1, ALDOA, B3GALT6, DSE, SLC25A1, SLC26A2, CHST14 |
| 96 | R-HSA-1630316 | Glycosaminoglycan metabolism | 71.42857 | CHST14, DSE, B3GALT6, SLC26A2 |
| 96 | GO:0044272 | sulfur compound biosynthetic process | 71.42857 | CHST14, SLC25A1, B3GALT6, DSE |
| 96 | GO:0046364 | monosaccharide biosynthetic process | 71.42857 | CHST14, SLC25A1, DSE |
| 96 | GO:0030203 | glycosaminoglycan metabolic process | 71.42857 | CHST14, B3GALT6, FUCA1, DSE |
| 96 | GO:0030166 | proteoglycan biosynthetic process | 71.42857 | CHST14, B3GALT6, DSE |
| 96 | GO:0016857 | racemase and epimerase activity, acting on carbohydrates and derivatives | 71.42857 | DSE |
| 96 | GO:0042301 | phosphate ion binding | 71.42857 | CHST14 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0004993 | 105 | Slender long bones with narrow diaphyses |
| HP:0007041 | 105 | Chronic lymphocytic meningitis |
| HP:0007333 | 105 | Hypoplasia of the frontal lobes |
| HP:0410292 | 105 | Abnormal isohemagglutinin level |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 105 | GO:0030258 | lipid modification | 100 | FIG4, SLC35C1, MFSD2A |
| 105 | R-HSA-446203 | Asparagine N-linked glycosylation | 75 | DPM1, TRAPPC10, SLC35C1, COPB2 |
| 105 | GO:0006493 | protein O-linked glycosylation | 75 | B3GALT6, SLC35C1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000501 | 126 | Glaucoma |
| HP:0000541 | 126 | Retinal detachment |
| HP:0000648 | 126 | Optic atrophy |
| HP:0001644 | 126 | Dilated cardiomyopathy |
| HP:0003560 | 126 | Muscular dystrophy |
| HP:0007260 | 126 | Type II lissencephaly |
| HP:0007973 | 126 | Retinal dysplasia |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 126 | GO:0035269 | protein O-linked mannosylation | 100.00000 | LARGE1, CRPPA, POMT1, DPM3, DPM1, POMGNT2, POMT2, FKTN, B4GAT1, RXYLT1, FKRP |
| 126 | hsa00515 | Mannose type O-glycan biosynthesis | 85.71429 | POMGNT2, POMT2, POMGNT1, POMK, FKRP, LARGE1, CRPPA, RXYLT1, POMT1, B4GAT1, B3GALNT2, FKTN |
| 126 | R-HSA-5173105 | O-linked glycosylation | 85.71429 | POMT2, POMGNT2, POMGNT1, DAG1, B3GALNT2, LARGE1, B4GAT1, POMK, POMT1 |
| 126 | R-HSA-5668914 | Diseases of metabolism | 85.71429 | IDUA, DPM3, DHDDS, DPM1, POMGNT1, DAG1, LARGE1, AHCY, MMUT, B4GAT1, IDS, POMT2, POMT1 |
| 126 | R-HSA-3906995 | Diseases associated with O-glycosylation of proteins | 85.71429 | POMGNT1, DAG1, LARGE1, B4GAT1, POMT2, POMT1 |
| 126 | GO:0071711 | basement membrane organization | 85.71429 | LARGE1, LAMA2, DAG1, POMGNT1, POMT2, LAMB1, COL4A1 |
| 126 | GO:0021542 | dentate gyrus development | 85.71429 | POMT2, LARGE1, POMGNT1 |
| 126 | R-HSA-3781865 | Diseases of glycosylation | 71.42857 | DPM3, DHDDS, POMGNT1, DAG1, LARGE1, DPM1, B4GAT1, POMT2, POMT1 |
| 126 | GO:0060049 | regulation of protein glycosylation | 71.42857 | POMT2, FKTN, POMT1 |
| 126 | GO:0150076 | neuroinflammatory response | 71.42857 | POMT2, LARGE1, POMGNT1 |
| 126 | GO:0008375 | acetylglucosaminyltransferase activity | 71.42857 | POMGNT1, POMGNT2, B4GAT1, LARGE1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000759 | 33 | Abnormal peripheral nervous system morphology |
| HP:0001929 | 33 | Reduced factor XI activity |
| HP:0003073 | 33 | Hypoalbuminemia |
| HP:0003256 | 33 | Abnormality of the coagulation cascade |
| HP:0003563 | 33 | Decreased LDL cholesterol concentration |
| HP:0003645 | 33 | Prolonged partial thromboplastin time |
| HP:0005543 | 33 | Reduced protein C activity |
| HP:0008151 | 33 | Prolonged prothrombin time |
| HP:0011327 | 33 | Posterior plagiocephaly |
| HP:0012340 | 33 | Decreased resting energy expenditure |
| HP:0012447 | 33 | Abnormal myelination |
| HP:0020037 | 33 | Astasia |
| HP:0025457 | 33 | Decreased CSF protein concentration |
| HP:0025458 | 33 | Decreased CSF albumin concentration |
| HP:0030194 | 33 | Fatigable weakness of speech muscles |
| HP:0030906 | 33 | Suck reflex |
| HP:0031146 | 33 | Impaired oral bolus formation |
| HP:0040209 | 33 | Decreased CSF biopterin level |
| HP:0100899 | 33 | Sclerosis of finger phalanx |
| HP:0410240 | 33 | Abnormal circulating IgA level |
| HP:0410242 | 33 | Abnormal circulating IgG level |
| HP:0410243 | 33 | Abnormal circulating IgM level |
| HP:0410295 | 33 | Complete or near-complete absence of specific antibody response to tetanus vaccine |
| HP:0410305 | 33 | Partial absence of specific antibody response to Haemophilus influenzae type b (Hib) vaccine |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 33 | R-HSA-446203 | Asparagine N-linked glycosylation | 91.66667 | COG8, MCFD2, NGLY1, COG2, GNE, B4GALT1, MPI, LMAN1, ALG8, ALG6, DDOST, PMM2, DPM1, MGAT2, F8, ALG12 |
| 33 | GO:0009100 | glycoprotein metabolic process | 83.33333 | B4GALT1, ALG8, DPM1, DDOST, NGLY1, ALG6, MGAT2, PMM2, ALG12 |
| 33 | GO:0006457 | protein folding | 79.16667 | LMAN1, ALG12, NGLY1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001234 | 125 | Hitchhiker thumb |
| HP:0001407 | 125 | Hepatic cysts |
| HP:0002265 | 125 | Large fleshy ears |
| HP:0003186 | 125 | Inverted nipples |
| HP:0008724 | 125 | Hypoplasia of the ovary |
| HP:0008776 | 125 | Abnormal renal artery morphology |
| HP:0009487 | 125 | Ulnar deviation of the hand |
| HP:0010763 | 125 | Low insertion of columella |
| HP:0012704 | 125 | Widened subarachnoid space |
| HP:0032464 | 125 | Ureteral hypoplasia |
| HP:0100865 | 125 | Broad ischia |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 125 | GO:0000030 | mannosyltransferase activity | 90.90909 | ALG11, ALG2, DPM1, ALG8, ALG9, ALG12, ALG3 |
| 125 | GO:0006488 | dolichol-linked oligosaccharide biosynthetic process | 81.81818 | MPDU1, ALG9, ALG8, DPM1, ALG2, RFT1, ALG12, ALG3 |
| 125 | GO:0019348 | dolichol metabolic process | 81.81818 | MPDU1, ALG9, ALG8, DPM1, ALG2, RFT1, ALG12, ALG3 |
| 125 | hsa00510 | N-Glycan biosynthesis | 72.72727 | ALG8, GANAB, ALG12, ALG11, ALG3, ALG5, ALG9, DPM1, ALG2, B4GALT1, MAN1B1, MGAT2 |
| 125 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 72.72727 | RFT1, ALG5, ALG2, ALG8, ALG9, ALG11, PMM2, DPM1, ALG3, MPDU1, ALG12 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000759 | 77 | Abnormal peripheral nervous system morphology |
| HP:0000969 | 77 | Edema |
| HP:0001929 | 77 | Reduced factor XI activity |
| HP:0001976 | 77 | Reduced antithrombin III activity |
| HP:0002401 | 77 | Stroke-like episode |
| HP:0003186 | 77 | Inverted nipples |
| HP:0003540 | 77 | Impaired platelet aggregation |
| HP:0003655 | 77 | Reduced level of N-acetylglucosaminyltransferase II |
| HP:0500173 | 77 | Reflex asystolic syncope |
| HP:0003256 | 77 | Abnormality of the coagulation cascade |
| HP:0003282 | 77 | Low alkaline phosphatase |
| HP:0003645 | 77 | Prolonged partial thromboplastin time |
| HP:0004523 | 77 | Long eyebrows |
| HP:0004855 | 77 | Reduced protein S activity |
| HP:0005543 | 77 | Reduced protein C activity |
| HP:0009124 | 77 | Abnormal adipose tissue morphology |
| HP:0010814 | 77 | Abnormal position of hair whorl |
| HP:0011327 | 77 | Posterior plagiocephaly |
| HP:0011858 | 77 | Reduced factor IX activity |
| HP:0012050 | 77 | Anasarca |
| HP:0012509 | 77 | Reduced thyroxin-binding globulin |
| HP:0012512 | 77 | Diffuse optic disc pallor |
| HP:0012882 | 77 | Hyperplastic labia majora |
| HP:0025330 | 77 | Downgaze palsy |
| HP:0025534 | 77 | Ocular melanocytosis |
| HP:0031404 | 77 | Impaired antigen-specific response |
| HP:0410240 | 77 | Abnormal circulating IgA level |
| HP:0410242 | 77 | Abnormal circulating IgG level |
| HP:0410243 | 77 | Abnormal circulating IgM level |
| HP:0410295 | 77 | Complete or near-complete absence of specific antibody response to tetanus vaccine |
| HP:0410305 | 77 | Partial absence of specific antibody response to Haemophilus influenzae type b (Hib) vaccine |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 77 | R-HSA-5668914 | Diseases of metabolism | 90.32258 | DPAGT1, ALG6, SRD5A3, ALG11, B4GALT1, DPM1, ALDOB, MGAT2, AHCY, RFT1, GNE, MPI, ALG3, MAN1B1, DPM3, DPM2, ALG8, PMM2, ALG12 |
| 77 | R-HSA-446203 | Asparagine N-linked glycosylation | 90.32258 | DPAGT1, ALG6, SRD5A3, ALG11, B4GALT1, DPM1, F8, MGAT2, RFT1, NGLY1, MCFD2, GNE, MPI, ALG3, DDOST, MAN1B1, COG2, DPM3, DPM2, LMAN1, ALG8, PMM2, ALG12 |
| 77 | R-HSA-3781865 | Diseases of glycosylation | 90.32258 | DPAGT1, SRD5A3, RFT1, DPM3, DPM2, GNE, B4GALT1, MPI, ALG8, ALG6, ALG11, PMM2, DPM1, ALG3, MGAT2, MAN1B1, ALG12 |
| 77 | GO:0006487 | protein N-linked glycosylation | 83.87097 | B4GALT1, SRD5A3, ALG8, DPM1, DDOST, ALG11, ALG6, MGAT2, DPAGT1, RFT1, PMM2, ALG12, ALG3 |
| 77 | hsa00510 | N-Glycan biosynthesis | 77.41935 | ALG6, ALG8, ALG12, ALG11, ALG3, DPM2, DDOST, DPM3, SRD5A3, DPM1, MAN1B1, DPAGT1, B4GALT1, MGAT2 |
| 77 | R-HSA-3781860 | Diseases associated with N-glycosylation of proteins | 77.41935 | DPAGT1, RFT1, ALG8, ALG6, ALG11, B4GALT1, ALG3, MGAT2, MAN1B1, ALG12 |
| 77 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 74.19355 | DPAGT1, SRD5A3, RFT1, DPM3, DPM2, GNE, MPI, ALG8, ALG6, ALG11, PMM2, DPM1, ALG3, ALG12 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001027 | 75 | Soft, doughy skin |
| HP:0002616 | 75 | Aortic root aneurysm |
| HP:0003016 | 75 | Metaphyseal widening |
| HP:0003414 | 75 | Atlantoaxial dislocation |
| HP:0004993 | 75 | Slender long bones with narrow diaphyses |
| HP:0005678 | 75 | Anterior atlanto-occipital dislocation |
| HP:0006522 | 75 | Repeated pneumothoraces |
| HP:0008807 | 75 | Acetabular dysplasia |
| HP:0012727 | 75 | Thoracic aortic aneurysm |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 75 | R-HSA-1638091 | Heparan sulfate/heparin (HS-GAG) metabolism | 88.88889 | B3GALT6, GLB1, XYLT1 |
| 75 | GO:0035250 | UDP-galactosyltransferase activity | 88.88889 | B3GALT6 |
| 75 | GO:0140103 | catalytic activity, acting on a glycoprotein | 88.88889 | B3GALT6 |
| 75 | GO:0005797 | Golgi medial cisterna | 88.88889 | B3GALT6 |
| 75 | hsa00534 | Glycosaminoglycan biosynthesis - heparan sulfate / heparin | 77.77778 | EXTL3, B3GALT6, XYLT1 |
| 75 | R-HSA-1793185 | Chondroitin sulfate/dermatan sulfate metabolism | 77.77778 | B3GALT6, DSE, CHST14, XYLT1 |
| 75 | R-HSA-1971475 | A tetrasaccharide linker sequence is required for GAG synthesis | 77.77778 | B3GALT6, XYLT1 |
| 75 | R-HSA-3560782 | Diseases associated with glycosaminoglycan metabolism | 77.77778 | B3GALT6, CHST14 |
| 75 | R-HSA-4420332 | Defective B3GALT6 causes EDSP2 and SEMDJL1 | 77.77778 | B3GALT6 |
| 75 | GO:1903510 | mucopolysaccharide metabolic process | 77.77778 | CHST14, DSE, GLB1, XYLT1, B3GALT6 |
| 75 | GO:0015012 | heparan sulfate proteoglycan biosynthetic process | 77.77778 | EXTL3, B3GALT6, XYLT1, DSE |
| HPO | Cluster | Description |
|---|---|---|
| HP:0003121 | 100 | Limb joint contracture |
| HP:0003186 | 100 | Inverted nipples |
| HP:0007366 | 100 | Atrophy/Degeneration affecting the brainstem |
| HP:0008695 | 100 | Transient nephrotic syndrome |
| HP:0012345 | 100 | Abnormal glycosylation |
| HP:0012348 | 100 | Decreased galactosylation of N-linked protein glycosylation |
| HP:0012363 | 100 | Decreased sialylation of O-linked protein glycosylation |
| HP:0012762 | 100 | Cerebral white matter atrophy |
| HP:0045060 | 100 | Aplasia/hypoplasia involving bones of the extremities |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 100 | GO:0015165 | pyrimidine nucleotide-sugar transmembrane transporter activity | 88.88889 | SLC35A2 |
| 100 | GO:0090481 | pyrimidine nucleotide-sugar transmembrane transport | 77.77778 | SLC35A2 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001374 | 124 | Congenital hip dislocation |
| HP:0001929 | 124 | Reduced factor XI activity |
| HP:0003121 | 124 | Limb joint contracture |
| HP:0003563 | 124 | Decreased LDL cholesterol concentration |
| HP:0005543 | 124 | Reduced protein C activity |
| HP:0012340 | 124 | Decreased resting energy expenditure |
| HP:0012447 | 124 | Abnormal myelination |
| HP:0020037 | 124 | Astasia |
| HP:0025457 | 124 | Decreased CSF protein concentration |
| HP:0025458 | 124 | Decreased CSF albumin concentration |
| HP:0030194 | 124 | Fatigable weakness of speech muscles |
| HP:0030906 | 124 | Suck reflex |
| HP:0031146 | 124 | Impaired oral bolus formation |
| HP:0040209 | 124 | Decreased CSF biopterin level |
| HP:0100899 | 124 | Sclerosis of finger phalanx |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 124 | R-HSA-532668 | N-glycan trimming in the ER and Calnexin/Calreticulin cycle | 86.66667 | NGLY1 |
| 124 | GO:0071712 | ER-associated misfolded protein catabolic process | 86.66667 | NGLY1 |
| 124 | GO:0006517 | protein deglycosylation | 86.66667 | NGLY1 |
| 124 | GO:0006516 | glycoprotein catabolic process | 86.66667 | NGLY1 |
| 124 | R-HSA-446203 | Asparagine N-linked glycosylation | 80.00000 | NGLY1, B4GALT1, MPI, ALG8, ALG6, PMM2, DPM1, MGAT2, ALG12 |
| 124 | GO:0016811 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | 80.00000 | NGLY1 |
| 124 | GO:0006457 | protein folding | 73.33333 | ALG12, NGLY1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001929 | 80 | Reduced factor XI activity |
| HP:0002243 | 80 | Protein-losing enteropathy |
| HP:0002625 | 80 | Deep venous thrombosis |
| HP:0003563 | 80 | Decreased LDL cholesterol concentration |
| HP:0004855 | 80 | Reduced protein S activity |
| HP:0005543 | 80 | Reduced protein C activity |
| HP:0006118 | 80 | Shortening of all distal phalanges of the fingers |
| HP:0011443 | 80 | Abnormality of coordination |
| HP:0011858 | 80 | Reduced factor IX activity |
| HP:0012509 | 80 | Reduced thyroxin-binding globulin |
| HP:0012882 | 80 | Hyperplastic labia majora |
| HP:0031404 | 80 | Impaired antigen-specific response |
| HP:0003073 | 80 | Hypoalbuminemia |
| HP:0040246 | 80 | Reduced antithrombin antigen |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 80 | GO:0006487 | protein N-linked glycosylation | 85.71429 | NUS1, B4GALT1, DHDDS, ALG8, DPM1, ALG1, ALG6, MGAT2, DPAGT1, PMM2, ALG12 |
| 80 | R-HSA-3781865 | Diseases of glycosylation | 78.57143 | DPAGT1, ALG1, B4GALT1, MPI, ALG8, ALG6, PMM2, DPM1, MGAT2, ALG12 |
| 80 | R-HSA-5668914 | Diseases of metabolism | 78.57143 | DPAGT1, ALG1, B4GALT1, MPI, ALG8, ALG6, MMACHC, MTRR, PMM2, DPM1, MGAT2, ALG12 |
| 80 | R-HSA-446203 | Asparagine N-linked glycosylation | 78.57143 | DPAGT1, COG8, NGLY1, ALG1, B4GALT1, MPI, ALG8, ALG6, PMM2, DPM1, MGAT2, ALG12 |
| 80 | R-HSA-5609975 | Diseases associated with glycosylation precursor biosynthesis | 78.57143 | DHDDS, NUS1, MPI, PMM2, DPM1 |
| 80 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 78.57143 | DPAGT1, ALG1, MPI, ALG8, ALG6, PMM2, DPM1, ALG12 |
| 80 | hsa00051 | Fructose and mannose metabolism | 71.42857 | PMM2, MPI |
| 80 | hsa01250 | Biosynthesis of nucleotide sugars | 71.42857 | PMM2, MPI |
| 80 | hsa00520 | Amino sugar and nucleotide sugar metabolism | 71.42857 | PMM2, MPI |
| 80 | R-HSA-446219 | Synthesis of substrates in N-glycan biosythesis | 71.42857 | DHDDS, NUS1, MPI, PMM2, DPM1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000895 | 99 | Lateral clavicle hook |
| HP:0005182 | 99 | Bicuspid pulmonary valve |
| HP:0008108 | 99 | Advanced tarsal ossification |
| HP:0008569 | 99 | Microtia, second degree |
| HP:0008873 | 99 | Disproportionate short-limb short stature |
| HP:0012107 | 99 | Increased fibular diameter |
| HP:0100819 | 99 | Intestinal fistula |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 99 | R-HSA-5668914 | Diseases of metabolism | 85.71429 | B3GLCT, SLC35D1 |
| 99 | GO:0019318 | hexose metabolic process | 85.71429 | INPPL1, B3GLCT |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000013 | 115 | Hypoplasia of the uterus |
| HP:0002761 | 115 | Generalized joint hypermobility |
| HP:0003164 | 115 | Hypothalamic gonadotropin-releasing hormone deficiency |
| HP:0003187 | 115 | Breast hypoplasia |
| HP:0005616 | 115 | Accelerated skeletal maturation |
| HP:0008724 | 115 | Hypoplasia of the ovary |
| HP:0030019 | 115 | Increased female libido |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 115 | R-HSA-373076 | Class A/1 (Rhodopsin-like receptors) | 85.71429 | GNRHR, PROK2, KISS1, TAC3, KISS1R, GNRH1, TACR3, PROKR2 |
| 115 | R-HSA-375276 | Peptide ligand-binding receptors | 85.71429 | PROK2, KISS1, TAC3, KISS1R, TACR3, PROKR2 |
| 115 | R-HSA-500792 | GPCR ligand binding | 85.71429 | GNRHR, WNT4, KISS1, PROK2, TAC3, DHH, KISS1R, GNRH1, TACR3, PROKR2 |
| 115 | R-HSA-416476 | G alpha (q) signalling events | 85.71429 | GNRHR, PROK2, KISS1, TAC3, KISS1R, GNRH1, TACR3, PROKR2 |
| 115 | hsa04929 | GnRH secretion | 71.42857 | KISS1, KISS1R, GNRH1 |
| 115 | hsa04080 | Neuroactive ligand-receptor interaction | 71.42857 | GNRHR, GNRH1, KISS1R, TAC3, TACR3, LEP, LEPR, KISS1 |
| 115 | R-HSA-375281 | Hormone ligand-binding receptors | 71.42857 | GNRHR, GNRH1 |
| 115 | GO:0045987 | positive regulation of smooth muscle contraction | 71.42857 | TACR3, PROK2 |
| 115 | GO:0048608 | reproductive structure development | 71.42857 | CHD7, WNT4, LEP, HESX1, NHLH2, FGF8, DHH, FOXL2, GNRH1, MKKS, ESR1, SCAPER |
| 115 | GO:0032274 | gonadotropin secretion | 71.42857 | GNRHR, KISS1, LEP, FOXL2 |
| 115 | GO:0007548 | sex differentiation | 71.42857 | CHD7, WNT4, CYP17A1, LEP, HESX1, NHLH2, FGF8, DHH, FOXL2, GNRH1, MKKS, ESR1, SCAPER |
| 115 | GO:0045777 | positive regulation of blood pressure | 71.42857 | TAC3, TACR3, PDE4D |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001302 | 60 | Pachygyria |
| HP:0002282 | 60 | Gray matter heterotopia |
| HP:0002350 | 60 | Cerebellar cyst |
| HP:0003325 | 60 | Limb-girdle muscle weakness |
| HP:0003560 | 60 | Muscular dystrophy |
| HP:0003707 | 60 | Calf muscle pseudohypertrophy |
| HP:0006899 | 60 | Fusion of the cerebellar hemispheres |
| HP:0007260 | 60 | Type II lissencephaly |
| HP:0030046 | 60 | Hypoglycosylation of alpha-dystroglycan |
| HP:0030099 | 60 | Reduced muscle fiber alpha dystroglycan |
| HP:0030197 | 60 | Fatigable weakness of skeletal muscles |
| HP:0040173 | 60 | Abnormality of the tongue muscle |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 60 | hsa00515 | Mannose type O-glycan biosynthesis | 83.33333 | FKTN, POMGNT2, POMGNT1, FKRP, LARGE1, CRPPA, RXYLT1, POMT1, B4GAT1, POMT2, POMK |
| 60 | R-HSA-5173105 | O-linked glycosylation | 83.33333 | POMK, POMGNT2, DAG1, POMGNT1, LARGE1, B4GAT1, POMT2, POMT1 |
| 60 | R-HSA-3781865 | Diseases of glycosylation | 83.33333 | GFPT1, DPM3, DPM1, DAG1, POMGNT1, LARGE1, ALG14, B4GAT1, POMT2, POMT1 |
| 60 | GO:0035269 | protein O-linked mannosylation | 83.33333 | LARGE1, POMT1, DPM3, DPM1, POMGNT2, POMT2, FKRP, FKTN, B4GAT1, RXYLT1, CRPPA |
| 60 | GO:0043403 | skeletal muscle tissue regeneration | 83.33333 | LARGE1, DAG1, CAPN3, SGCA, FKRP |
| 60 | R-HSA-3906995 | Diseases associated with O-glycosylation of proteins | 75.00000 | POMGNT1, DAG1, LARGE1, B4GAT1, POMT2, POMT1 |
| 60 | GO:0071711 | basement membrane organization | 75.00000 | LARGE1, LAMA2, DAG1, LAMA1, POMGNT1, POMT2, LAMB1 |
| 60 | GO:0060049 | regulation of protein glycosylation | 75.00000 | POMT2, FKTN, POMT1 |
| 60 | GO:0002162 | dystroglycan binding | 75.00000 | DAG1, FKRP |
| HPO | Cluster | Description |
|---|---|---|
| HP:0002947 | 68 | Cervical kyphosis |
| HP:0003498 | 68 | Disproportionate short stature |
| HP:0004002 | 68 | Flattened radial epiphyses |
| HP:0004037 | 68 | Abnormal ulnar epiphysis morphology |
| HP:0005922 | 68 | Abnormal hand morphology |
| HP:0008434 | 68 | Hypoplastic cervical vertebrae |
| HP:0008807 | 68 | Acetabular dysplasia |
| HP:0008829 | 68 | Delayed femoral head ossification |
| HP:0009381 | 68 | Short finger |
| HP:0009487 | 68 | Ulnar deviation of the hand |
| HP:0025264 | 68 | Stiff ankle |
| HP:0040072 | 68 | Abnormal forearm bone morphology |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 68 | GO:0035988 | chondrocyte proliferation | 83.33333 | MMP14, SLC26A2, EXT1, NPR2 |
| 68 | GO:0019532 | oxalate transport | 75.00000 | SLC26A2 |
| 68 | GO:0015701 | bicarbonate transport | 75.00000 | SLC26A2 |
| 68 | GO:1902358 | sulfate transmembrane transport | 75.00000 | SLC26A2 |
| 68 | GO:0002062 | chondrocyte differentiation | 75.00000 | EXT1, NPR2, SLC26A2, EXT2, COL2A1, WNT7A |
| 68 | GO:0019531 | oxalate transmembrane transporter activity | 75.00000 | SLC26A2 |
| 68 | GO:0008271 | secondary active sulfate transmembrane transporter activity | 75.00000 | SLC26A2 |
| 68 | GO:0015106 | bicarbonate transmembrane transporter activity | 75.00000 | SLC26A2 |
| 68 | GO:0005452 | solute:inorganic anion antiporter activity | 75.00000 | SLC26A2 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0005543 | 87 | Reduced protein C activity |
| HP:0010819 | 87 | Atonic seizure |
| HP:0011812 | 87 | Agraphesthesia |
| HP:0012340 | 87 | Decreased resting energy expenditure |
| HP:0020037 | 87 | Astasia |
| HP:0025457 | 87 | Decreased CSF protein concentration |
| HP:0025458 | 87 | Decreased CSF albumin concentration |
| HP:0030194 | 87 | Fatigable weakness of speech muscles |
| HP:0030906 | 87 | Suck reflex |
| HP:0031146 | 87 | Impaired oral bolus formation |
| HP:0040209 | 87 | Decreased CSF biopterin level |
| HP:0100899 | 87 | Sclerosis of finger phalanx |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 87 | R-HSA-532668 | N-glycan trimming in the ER and Calnexin/Calreticulin cycle | 83.33333 | NGLY1 |
| 87 | R-HSA-446203 | Asparagine N-linked glycosylation | 83.33333 | NGLY1, MPI, ALG8, ALG6, B4GALT1, DPM1, ALG12 |
| 87 | GO:0071712 | ER-associated misfolded protein catabolic process | 83.33333 | NGLY1 |
| 87 | GO:0006457 | protein folding | 83.33333 | ALG12, NGLY1 |
| 87 | GO:0006517 | protein deglycosylation | 83.33333 | NGLY1 |
| 87 | GO:0006516 | glycoprotein catabolic process | 83.33333 | NGLY1 |
| 87 | GO:0016811 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | 83.33333 | NGLY1 |
| 87 | hsa04141 | Protein processing in endoplasmic reticulum | 75.00000 | NGLY1 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001234 | 79 | Hitchhiker thumb |
| HP:0001591 | 79 | Bell-shaped thorax |
| HP:0002947 | 79 | Cervical kyphosis |
| HP:0003026 | 79 | Short long bone |
| HP:0003498 | 79 | Disproportionate short stature |
| HP:0004002 | 79 | Flattened radial epiphyses |
| HP:0004037 | 79 | Abnormal ulnar epiphysis morphology |
| HP:0004664 | 79 | Facial midline hemangioma |
| HP:0006385 | 79 | Short lower limbs |
| HP:0008434 | 79 | Hypoplastic cervical vertebrae |
| HP:0008829 | 79 | Delayed femoral head ossification |
| HP:0009824 | 79 | Upper limb undergrowth |
| HP:0012427 | 79 | Increased femoral anteversion |
| HP:0009826 | 79 | Limb undergrowth |
| HP:0025264 | 79 | Stiff ankle |
| HP:0040072 | 79 | Abnormal forearm bone morphology |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 79 | GO:0001503 | ossification | 81.25 | EXT1, NPR2, SLC26A2, EXT2, XYLT1, COL2A1, MMP13, CSGALNACT1, COMP, EBP, PHEX |
| 79 | GO:0002062 | chondrocyte differentiation | 81.25 | EXT1, NPR2, SLC26A2, EXT2, COL2A1, WNT7A, COMP |
| 79 | GO:0035988 | chondrocyte proliferation | 81.25 | SLC26A2, NPR2, EXT1, COMP |
| 79 | GO:0019531 | oxalate transmembrane transporter activity | 75.00 | SLC26A2 |
| 79 | GO:0008271 | secondary active sulfate transmembrane transporter activity | 75.00 | SLC26A2 |
| 79 | GO:0015106 | bicarbonate transmembrane transporter activity | 75.00 | SLC26A2 |
| 79 | GO:0005452 | solute:inorganic anion antiporter activity | 75.00 | SLC26A2 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0003256 | 84 | Abnormality of the coagulation cascade |
| HP:0012301 | 84 | Type II transferrin isoform profile |
| HP:0012347 | 84 | Abnormal protein N-linked glycosylation |
| HP:0012358 | 84 | Abnormal protein O-linked glycosylation |
| HP:0100874 | 84 | Thick hair |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 84 | R-HSA-446203 | Asparagine N-linked glycosylation | 80 | COG2, MPI, COG1, COG4, ALG8, ALG6, B4GALT1, DDOST, MAN1B1, COG7, ALG12 |
| 84 | GO:0007030 | Golgi organization | 80 | COG7, COG4, VPS13B, COG1 |
| 84 | GO:0070085 | glycosylation | 80 | COG7, B4GALT1, ALG8, COG1, COG4, ALG6, DDOST, ALG12, SLC39A8, COG2 |
| 84 | GO:0006891 | intra-Golgi vesicle-mediated transport | 80 | COG7, COG4, COG1 |
| 84 | GO:0099023 | vesicle tethering complex | 80 | COG4, VPS33A, COG1, COG7 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001762 | 103 | Talipes equinovarus |
| HP:0003311 | 103 | Hypoplasia of the odontoid process |
| HP:0004582 | 103 | Irregularity of vertebral bodies |
| HP:0011995 | 103 | Atrial septal dilatation |
| HP:0012301 | 103 | Type II transferrin isoform profile |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 103 | R-HSA-6807878 | COPI-mediated anterograde transport | 80 | COG7, COG4, COG1 |
| 103 | R-HSA-6811440 | Retrograde transport at the Trans-Golgi-Network | 80 | COG7, COG4, COG1 |
| 103 | R-HSA-199977 | ER to Golgi Anterograde Transport | 80 | COG7, COG4, COG1, TRAPPC2 |
| 103 | R-HSA-6811438 | Intra-Golgi traffic | 80 | COG7, COG4, COG1 |
| 103 | R-HSA-948021 | Transport to the Golgi and subsequent modification | 80 | TRAPPC2, COG1, COG4, B4GALT1, COG7 |
| 103 | GO:0099023 | vesicle tethering complex | 80 | TRAPPC2, COG4, COG1, COG7 |
| 103 | GO:0032588 | trans-Golgi network membrane | 80 | COG4, COG1, COG7 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000565 | 106 | Esotropia |
| HP:0000973 | 106 | Cutis laxa |
| HP:0001374 | 106 | Congenital hip dislocation |
| HP:0001476 | 106 | Delayed closure of the anterior fontanelle |
| HP:0001976 | 106 | Reduced antithrombin III activity |
| HP:0002240 | 106 | Hepatomegaly |
| HP:0002761 | 106 | Generalized joint hypermobility |
| HP:0003160 | 106 | Abnormal isoelectric focusing of serum transferrin |
| HP:0003186 | 106 | Inverted nipples |
| HP:0003199 | 106 | Decreased muscle mass |
| HP:0004993 | 106 | Slender long bones with narrow diaphyses |
| HP:0005272 | 106 | Prominent nasolabial fold |
| HP:0006114 | 106 | Multiple palmar creases |
| HP:0006891 | 106 | Thick cerebral cortex |
| HP:0007392 | 106 | Excessive wrinkled skin |
| HP:0007457 | 106 | Prominent veins on trunk |
| HP:0007552 | 106 | Abnormal subcutaneous fat tissue distribution |
| HP:0008113 | 106 | Multiple plantar creases |
| HP:0009125 | 106 | Lipodystrophy |
| HP:0010989 | 106 | Abnormality of the intrinsic pathway |
| HP:0011003 | 106 | High myopia |
| HP:0011995 | 106 | Atrial septal dilatation |
| HP:0025167 | 106 | Fragmented elastic fibers in the dermis |
| HP:0025244 | 106 | Subretinal pigment epithelium hemorrhage |
| HP:0012050 | 106 | Anasarca |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 106 | R-HSA-917977 | Transferrin endocytosis and recycling | 80 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 106 | R-HSA-77387 | Insulin receptor recycling | 80 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 106 | R-HSA-1222556 | ROS and RNS production in phagocytes | 80 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 106 | GO:0046961 | proton-transporting ATPase activity, rotational mechanism | 80 | ATP6V1A, ATP6V1E1, ATP6V0A2 |
| 106 | hsa04966 | Collecting duct acid secretion | 76 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 106 | hsa05110 | Vibrio cholerae infection | 76 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 106 | R-HSA-917937 | Iron uptake and transport | 76 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 106 | R-HSA-74752 | Signaling by Insulin receptor | 76 | GRB10, ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 106 | GO:0051117 | ATPase binding | 76 | ATP6V1E1, ATP6V0A2 |
| 106 | GO:0000220 | vacuolar proton-transporting V-type ATPase, V0 domain | 76 | ATP6V0A2 |
| 106 | GO:1904949 | ATPase complex | 76 | ATP6V1A, ATP6V0A2, ATP6V1E1, SMARCA2 |
| 106 | hsa05323 | Rheumatoid arthritis | 72 | ATP6V1E1, ATP6V1A, TGFB1, ATP6V0A2 |
| 106 | hsa04721 | Synaptic vesicle cycle | 72 | SNAP25, CPLX1, ATP6V1E1, ATP6V0A2, ATP6V1A |
| 106 | hsa05120 | Epithelial cell signaling in Helicobacter pylori infection | 72 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 106 | GO:0015078 | proton transmembrane transporter activity | 72 | ATP6V1A, ATP6V1E1, ATP6V0A2, SLC9A6 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000707 | 107 | Abnormality of the nervous system |
| HP:0000759 | 107 | Abnormal peripheral nervous system morphology |
| HP:0000969 | 107 | Edema |
| HP:0001410 | 107 | Decreased liver function |
| HP:0001929 | 107 | Reduced factor XI activity |
| HP:0002243 | 107 | Protein-losing enteropathy |
| HP:0002910 | 107 | Elevated circulating hepatic transaminase concentration |
| HP:0003073 | 107 | Hypoalbuminemia |
| HP:0003256 | 107 | Abnormality of the coagulation cascade |
| HP:0003563 | 107 | Decreased LDL cholesterol concentration |
| HP:0003645 | 107 | Prolonged partial thromboplastin time |
| HP:0004855 | 107 | Reduced protein S activity |
| HP:0005543 | 107 | Reduced protein C activity |
| HP:0009124 | 107 | Abnormal adipose tissue morphology |
| HP:0010557 | 107 | Overlapping fingers |
| HP:0011327 | 107 | Posterior plagiocephaly |
| HP:0012379 | 107 | Abnormal circulating enzyme concentration or activity |
| HP:0040246 | 107 | Reduced antithrombin antigen |
| HP:0410240 | 107 | Abnormal circulating IgA level |
| HP:0410242 | 107 | Abnormal circulating IgG level |
| HP:0410243 | 107 | Abnormal circulating IgM level |
| HP:0410295 | 107 | Complete or near-complete absence of specific antibody response to tetanus vaccine |
| HP:0410305 | 107 | Partial absence of specific antibody response to Haemophilus influenzae type b (Hib) vaccine |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 107 | hsa00510 | N-Glycan biosynthesis | 78.26087 | ALG6, ALG8, ALG12, ALG11, ALG1, ALG3, DDOST, DPM1, MOGS, DPAGT1, B4GALT1, MGAT2 |
| 107 | R-HSA-3781860 | Diseases associated with N-glycosylation of proteins | 78.26087 | DPAGT1, ALG1, MOGS, ALG11, ALG8, ALG6, ALG3, B4GALT1, MGAT2, ALG12 |
| 107 | R-HSA-3781865 | Diseases of glycosylation | 78.26087 | DPAGT1, ALG1, GNE, ALG11, B4GALT1, MOGS, MPI, ALG8, ALG6, ALG3, PMM2, DPM1, MGAT2, ALG12 |
| 107 | GO:0006487 | protein N-linked glycosylation | 78.26087 | B4GALT1, ALG8, DPM1, DDOST, ALG1, ALG11, ALG6, MGAT2, DPAGT1, MOGS, PMM2, ALG12, ALG3 |
| 107 | hsa00513 | Various types of N-glycan biosynthesis | 73.91304 | ALG12, ALG11, ALG1, ALG3, DDOST, B4GALT1, MGAT2 |
| 107 | R-HSA-5668914 | Diseases of metabolism | 73.91304 | DPAGT1, ALG1, GNE, ALG11, B4GALT1, MPI, ALG8, ALG6, ALG3, PMM2, DPM1, ALDOB, MGAT2, ALG12 |
| 107 | R-HSA-446203 | Asparagine N-linked glycosylation | 73.91304 | DPAGT1, ALG6, ALG1, ALG11, B4GALT1, DPM1, F8, COG8, MGAT2, MCFD2, NGLY1, GNE, MPI, ALG3, DDOST, COG2, LMAN1, ALG8, PMM2, ALG12 |
| 107 | R-HSA-446193 | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 73.91304 | DPAGT1, ALG1, GNE, ALG11, MPI, ALG8, ALG6, ALG3, PMM2, DPM1, ALG12 |
| 107 | GO:0070085 | glycosylation | 73.91304 | COG8, B4GALT1, ALG8, DPM1, DDOST, ALG1, ALG11, ALG6, MGAT2, DPAGT1, PMM2, ALG12, ALG3, COG2 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0002350 | 66 | Cerebellar cyst |
| HP:0002515 | 66 | Waddling gait |
| HP:0002938 | 66 | Lumbar hyperlordosis |
| HP:0003236 | 66 | Elevated circulating creatine kinase concentration |
| HP:0003325 | 66 | Limb-girdle muscle weakness |
| HP:0003403 | 66 | EMG: decremental response of compound muscle action potential to repetitive nerve stimulation |
| HP:0003551 | 66 | Difficulty climbing stairs |
| HP:0003560 | 66 | Muscular dystrophy |
| HP:0003691 | 66 | Scapular winging |
| HP:0003707 | 66 | Calf muscle pseudohypertrophy |
| HP:0008981 | 66 | Calf muscle hypertrophy |
| HP:0030099 | 66 | Reduced muscle fiber alpha dystroglycan |
| HP:0030046 | 66 | Hypoglycosylation of alpha-dystroglycan |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 66 | GO:0006486 | protein glycosylation | 76.92308 | LARGE1, CRPPA, POMT1, DPM3, GFPT1, ALG2, POMGNT1, DPM1, POMGNT2, POMT2, POMK, DPAGT1, FKTN, GMPPB, RXYLT1, B4GAT1, FKRP, ALG14 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001250 | 8 | Seizure |
| HP:0001508 | 8 | Failure to thrive |
| HP:0002120 | 8 | Cerebral cortical atrophy |
| HP:0002401 | 8 | Stroke-like episode |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 8 | GO:0048568 | embryonic organ development | 75 | MYO7A, PTCH1, GLI2, SIX3, NODAL, ERCC2, FGF8, DLL1, ERCC3, FOXH1, STIL |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001272 | 39 | Cerebellar atrophy |
| HP:0002020 | 39 | Gastroesophageal reflux |
| HP:0008676 | 39 | Congenital megaureter |
| HP:0010804 | 39 | Tented upper lip vermilion |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 39 | GO:0006664 | glycolipid metabolic process | 75 | PIGT, CLN6, FA2H, PIGN |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001928 | 71 | Abnormality of coagulation |
| HP:0003642 | 71 | Type I transferrin isoform profile |
| HP:0005478 | 71 | Prominent frontal sinuses |
| HP:0008529 | 71 | Absence of acoustic reflex |
| HP:0001976 | 71 | Reduced antithrombin III activity |
| HP:0002240 | 71 | Hepatomegaly |
| HP:0002910 | 71 | Elevated circulating hepatic transaminase concentration |
| HP:0012704 | 71 | Widened subarachnoid space |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 71 | GO:0006488 | dolichol-linked oligosaccharide biosynthetic process | 75 | SRD5A3, MPDU1, ALG8, ALG2, DPM1, ALG9, ALG6, DPAGT1, RFT1, DOLK |
| 71 | GO:0019348 | dolichol metabolic process | 75 | SRD5A3, MPDU1, ALG8, ALG2, DPM2, DPM1, ALG9, ALG6, DPAGT1, RFT1, DOLK |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001929 | 122 | Reduced factor XI activity |
| HP:0002361 | 122 | Psychomotor deterioration |
| HP:0010989 | 122 | Abnormality of the intrinsic pathway |
| HP:0025244 | 122 | Subretinal pigment epithelium hemorrhage |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 122 | hsa04966 | Collecting duct acid secretion | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa04145 | Phagosome | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa05165 | Human papillomavirus infection | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa04150 | mTOR signaling pathway | 75 | ATP6V1A, ATP6V1E1 |
| 122 | hsa05323 | Rheumatoid arthritis | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa00190 | Oxidative phosphorylation | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa05110 | Vibrio cholerae infection | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa04721 | Synaptic vesicle cycle | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | hsa05120 | Epithelial cell signaling in Helicobacter pylori infection | 75 | ATP6V1E1, ATP6V1A, ATP6V0A2 |
| 122 | R-HSA-917977 | Transferrin endocytosis and recycling | 75 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-74752 | Signaling by Insulin receptor | 75 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-9711097 | Cellular response to starvation | 75 | ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-917937 | Iron uptake and transport | 75 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-77387 | Insulin receptor recycling | 75 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-1222556 | ROS and RNS production in phagocytes | 75 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-983712 | Ion channel transport | 75 | ATP6V0A2, ATP6V1A, ATP6V1E1 |
| 122 | R-HSA-9639288 | Amino acids regulate mTORC1 | 75 | ATP6V1A, ATP6V1E1 |
| 122 | GO:0036295 | cellular response to increased oxygen levels | 75 | ATP6V0A2, ATP6V1A |
| 122 | GO:0007035 | vacuolar acidification | 75 | ATP6V0A2, ATP6V1A |
| 122 | GO:0061795 | Golgi lumen acidification | 75 | ATP6V0A2, ATP6V1A |
| 122 | GO:0097401 | synaptic vesicle lumen acidification | 75 | ATP6V1E1, ATP6V1A |
| 122 | GO:0016241 | regulation of macroautophagy | 75 | ATP6V1E1, ATP6V0A2, ATP6V1A |
| 122 | GO:0006879 | intracellular iron ion homeostasis | 75 | ATP6V0A2, ATP6V1A |
| 122 | GO:0046961 | proton-transporting ATPase activity, rotational mechanism | 75 | ATP6V1A, ATP6V1E1, ATP6V0A2 |
| 122 | GO:0051117 | ATPase binding | 75 | ATP6V1E1, ATP6V0A2 |
| 122 | GO:0046933 | proton-transporting ATP synthase activity, rotational mechanism | 75 | ATP6V1A |
| 122 | GO:0016324 | apical plasma membrane | 75 | ATP6V1A, ATP6V1E1 |
| 122 | GO:0098850 | extrinsic component of synaptic vesicle membrane | 75 | ATP6V1A |
| 122 | GO:0005902 | microvillus | 75 | ATP6V1A, ATP6V1E1 |
| 122 | GO:0030665 | clathrin-coated vesicle membrane | 75 | ATP6V1A, ATP6V1E1 |
| 122 | GO:1904949 | ATPase complex | 75 | ATP6V1A, ATP6V0A2, ATP6V1E1 |
| 122 | GO:0000220 | vacuolar proton-transporting V-type ATPase, V0 domain | 75 | ATP6V0A2 |
| 122 | GO:0005765 | lysosomal membrane | 75 | ATP6V1A, ATP6V0A2, ATP6V1E1 |
| 122 | GO:0000221 | vacuolar proton-transporting V-type ATPase, V1 domain | 75 | ATP6V1A, ATP6V1E1 |
| 122 | GO:1902495 | transmembrane transporter complex | 75 | ATP6V1A, ATP6V0A2, SCN8A, KCNQ3 |
| HPO | Cluster | Description |
|---|---|---|
| HP:0001644 | 91 | Dilated cardiomyopathy |
| HP:0003236 | 91 | Elevated circulating creatine kinase concentration |
| HP:0003325 | 91 | Limb-girdle muscle weakness |
| HP:0003551 | 91 | Difficulty climbing stairs |
| HP:0003560 | 91 | Muscular dystrophy |
| HP:0003691 | 91 | Scapular winging |
| HP:0003697 | 91 | Scapuloperoneal amyotrophy |
| HP:0003733 | 91 | Thigh hypertrophy |
| HP:0008981 | 91 | Calf muscle hypertrophy |
| HP:0025169 | 91 | Left ventricular systolic dysfunction |
| HP:0030092 | 91 | Reduced muscle fiber merosin |
| HP:0030099 | 91 | Reduced muscle fiber alpha dystroglycan |
| HP:0030197 | 91 | Fatigable weakness of skeletal muscles |
| HP:0040173 | 91 | Abnormality of the tongue muscle |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 91 | GO:0035269 | protein O-linked mannosylation | 71.42857 | LARGE1, CRPPA, POMT1, DPM3, DPM1, POMGNT2, POMT2, FKTN, B4GAT1, RXYLT1, FKRP |
| HPO | Cluster | Description |
|---|---|---|
| HP:0002283 | 94 | Global brain atrophy |
| HP:0003282 | 94 | Low alkaline phosphatase |
| HP:0008676 | 94 | Congenital megaureter |
| HP:0009824 | 94 | Upper limb undergrowth |
| HP:0010818 | 94 | Generalized tonic seizure |
| HP:0010850 | 94 | EEG with spike-wave complexes |
| HP:0025330 | 94 | Downgaze palsy |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 94 | hsa00563 | Glycosylphosphatidylinositol (GPI)-anchor biosynthesis | 71.42857 | PIGO, PIGP, PIGQ, PIGV, PIGW, PIGL, PIGN, PIGY, PIGT |
| 94 | R-HSA-163125 | Post-translational modification: synthesis of GPI-anchored proteins | 71.42857 | PIGO, PIGP, PIGW, PIGT, PIGY, DPM1, PIGV, PIGL, PIGN, PIGQ |
| 94 | GO:0006506 | GPI anchor biosynthetic process | 71.42857 | PGAP3, PIGP, PIGT, DPM1, PIGO, PIGL, PIGV, PIGQ, PIGN, PIGW, PGAP2, PIGY |
| 94 | GO:0140534 | endoplasmic reticulum protein-containing complex | 71.42857 | PIGQ, PIGP, PIGY, PIGT |
| 94 | GO:0008303 | caspase complex | 71.42857 | PIGT |
| HPO | Cluster | Description |
|---|---|---|
| HP:0000218 | 116 | High palate |
| HP:0001265 | 116 | Hyporeflexia |
| HP:0001385 | 116 | Hip dysplasia |
| HP:0002421 | 116 | Poor head control |
| HP:0002515 | 116 | Waddling gait |
| HP:0002650 | 116 | Scoliosis |
| HP:0003403 | 116 | EMG: decremental response of compound muscle action potential to repetitive nerve stimulation |
| HP:0003236 | 116 | Elevated circulating creatine kinase concentration |
| HP:0012762 | 116 | Cerebral white matter atrophy |
| HP:0003691 | 116 | Scapular winging |
| Cluster | Cell function | Description | Phenotype_coverage | Genes |
|---|---|---|---|---|
| 116 | GO:0042692 | muscle cell differentiation | 70 | ACTA1, LARGE1, NEB, BIN1, SPEG, KLHL41, CDON, SYNE1, DMD, FGFR2, CHRNB1, LAMB2, DLL1, SELENON, COMP, KCNH1, SHH, RYR1 |
| 116 | GO:0007517 | muscle organ development | 70 | LARGE1, NEB, DAG1, CDON, DISP1, CHRNA1, COL6A3, ACTA1, MTM1, CHRND, SMAD3, DMD, FGF8, DLL1, FOXH1, SHH, SPEG, FGFR2, SELENON, KLHL41, RYR1 |